vcf_clone_detect.py results for M. capitata RNA-seq samplesSetup R env. Load packages and set default image export formats, size and resolution.
knitr::opts_chunk$set(echo = TRUE,
fig.height = 12,
fig.width = 12,
dev = c("png", "pdf"),
dpi = 1000)
library(readxl)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
library(reshape2)
library(RcppCNPy)
library(tibble)
library(ggdendro)
library(cowplot)
library(RColorBrewer)
library(viridis)
## Loading required package: viridisLite
library(knitr)
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(phylogram)
options(scipen = 999) #Prevent scientific notation
cexSize <- 0.3
Load file with annotation for each sample.
samples.info <- read.table("../../samples_Mcapitata.annotations.txt", header=T, comment.char='')
rownames(samples.info) <- samples.info$sample
samples.info
## sample species treatment timepoint
## Mcapitata_ATAC_TP11_2302 Mcapitata_ATAC_TP11_2302 Mcapitata ATAC TP11
## Mcapitata_HTAC_TP11_2380 Mcapitata_HTAC_TP11_2380 Mcapitata HTAC TP11
## Mcapitata_ATAC_TP6_2402 Mcapitata_ATAC_TP6_2402 Mcapitata ATAC TP6
## Mcapitata_ATAC_TP12_2403 Mcapitata_ATAC_TP12_2403 Mcapitata ATAC TP12
## Mcapitata_ATAC_TP1_1037 Mcapitata_ATAC_TP1_1037 Mcapitata ATAC TP1
## Mcapitata_ATAC_TP1_1600 Mcapitata_ATAC_TP1_1600 Mcapitata ATAC TP1
## Mcapitata_ATAC_TP1_1652 Mcapitata_ATAC_TP1_1652 Mcapitata ATAC TP1
## Mcapitata_ATAC_TP3_1101 Mcapitata_ATAC_TP3_1101 Mcapitata ATAC TP3
## Mcapitata_ATAC_TP3_1548 Mcapitata_ATAC_TP3_1548 Mcapitata ATAC TP3
## Mcapitata_ATAC_TP3_1628 Mcapitata_ATAC_TP3_1628 Mcapitata ATAC TP3
## Mcapitata_ATAC_TP4_1108 Mcapitata_ATAC_TP4_1108 Mcapitata ATAC TP4
## Mcapitata_ATAC_TP4_1609 Mcapitata_ATAC_TP4_1609 Mcapitata ATAC TP4
## Mcapitata_ATAC_TP4_1651 Mcapitata_ATAC_TP4_1651 Mcapitata ATAC TP4
## Mcapitata_ATAC_TP5_1196 Mcapitata_ATAC_TP5_1196 Mcapitata ATAC TP5
## Mcapitata_ATAC_TP5_1610 Mcapitata_ATAC_TP5_1610 Mcapitata ATAC TP5
## Mcapitata_ATAC_TP5_1776 Mcapitata_ATAC_TP5_1776 Mcapitata ATAC TP5
## Mcapitata_ATAC_TP6_1114 Mcapitata_ATAC_TP6_1114 Mcapitata ATAC TP6
## Mcapitata_ATAC_TP6_1611 Mcapitata_ATAC_TP6_1611 Mcapitata ATAC TP6
## Mcapitata_ATAC_TP7_1058 Mcapitata_ATAC_TP7_1058 Mcapitata ATAC TP7
## Mcapitata_ATAC_TP7_1455 Mcapitata_ATAC_TP7_1455 Mcapitata ATAC TP7
## Mcapitata_ATAC_TP7_1499 Mcapitata_ATAC_TP7_1499 Mcapitata ATAC TP7
## Mcapitata_ATAC_TP8_1083 Mcapitata_ATAC_TP8_1083 Mcapitata ATAC TP8
## Mcapitata_ATAC_TP8_1436 Mcapitata_ATAC_TP8_1436 Mcapitata ATAC TP8
## Mcapitata_ATAC_TP8_1779 Mcapitata_ATAC_TP8_1779 Mcapitata ATAC TP8
## Mcapitata_ATAC_TP9_1121 Mcapitata_ATAC_TP9_1121 Mcapitata ATAC TP9
## Mcapitata_ATAC_TP9_1420 Mcapitata_ATAC_TP9_1420 Mcapitata ATAC TP9
## Mcapitata_ATAC_TP9_1580 Mcapitata_ATAC_TP9_1580 Mcapitata ATAC TP9
## Mcapitata_ATAC_TP10_1095 Mcapitata_ATAC_TP10_1095 Mcapitata ATAC TP10
## Mcapitata_ATAC_TP10_1561 Mcapitata_ATAC_TP10_1561 Mcapitata ATAC TP10
## Mcapitata_ATAC_TP10_1631 Mcapitata_ATAC_TP10_1631 Mcapitata ATAC TP10
## Mcapitata_ATAC_TP11_1076 Mcapitata_ATAC_TP11_1076 Mcapitata ATAC TP11
## Mcapitata_ATAC_TP11_1644 Mcapitata_ATAC_TP11_1644 Mcapitata ATAC TP11
## Mcapitata_ATAC_TP12_1120 Mcapitata_ATAC_TP12_1120 Mcapitata ATAC TP12
## Mcapitata_ATAC_TP12_1452 Mcapitata_ATAC_TP12_1452 Mcapitata ATAC TP12
## Mcapitata_ATHC_TP1_1218 Mcapitata_ATHC_TP1_1218 Mcapitata ATHC TP1
## Mcapitata_ATHC_TP1_1826 Mcapitata_ATHC_TP1_1826 Mcapitata ATHC TP1
## Mcapitata_ATHC_TP1_2068 Mcapitata_ATHC_TP1_2068 Mcapitata ATHC TP1
## Mcapitata_ATHC_TP3_1544 Mcapitata_ATHC_TP3_1544 Mcapitata ATHC TP3
## Mcapitata_ATHC_TP3_2731 Mcapitata_ATHC_TP3_2731 Mcapitata ATHC TP3
## Mcapitata_ATHC_TP3_2866 Mcapitata_ATHC_TP3_2866 Mcapitata ATHC TP3
## Mcapitata_ATHC_TP4_1221 Mcapitata_ATHC_TP4_1221 Mcapitata ATHC TP4
## Mcapitata_ATHC_TP4_2561 Mcapitata_ATHC_TP4_2561 Mcapitata ATHC TP4
## Mcapitata_ATHC_TP4_2734 Mcapitata_ATHC_TP4_2734 Mcapitata ATHC TP4
## Mcapitata_ATHC_TP5_1229 Mcapitata_ATHC_TP5_1229 Mcapitata ATHC TP5
## Mcapitata_ATHC_TP5_1706 Mcapitata_ATHC_TP5_1706 Mcapitata ATHC TP5
## Mcapitata_ATHC_TP5_2986 Mcapitata_ATHC_TP5_2986 Mcapitata ATHC TP5
## Mcapitata_ATHC_TP6_1212 Mcapitata_ATHC_TP6_1212 Mcapitata ATHC TP6
## Mcapitata_ATHC_TP6_2016 Mcapitata_ATHC_TP6_2016 Mcapitata ATHC TP6
## Mcapitata_ATHC_TP6_2555 Mcapitata_ATHC_TP6_2555 Mcapitata ATHC TP6
## Mcapitata_ATHC_TP7_1223 Mcapitata_ATHC_TP7_1223 Mcapitata ATHC TP7
## Mcapitata_ATHC_TP7_2860 Mcapitata_ATHC_TP7_2860 Mcapitata ATHC TP7
## Mcapitata_ATHC_TP7_2875 Mcapitata_ATHC_TP7_2875 Mcapitata ATHC TP7
## Mcapitata_ATHC_TP8_1260 Mcapitata_ATHC_TP8_1260 Mcapitata ATHC TP8
## Mcapitata_ATHC_TP8_2735 Mcapitata_ATHC_TP8_2735 Mcapitata ATHC TP8
## Mcapitata_ATHC_TP8_2753 Mcapitata_ATHC_TP8_2753 Mcapitata ATHC TP8
## Mcapitata_ATHC_TP9_1148 Mcapitata_ATHC_TP9_1148 Mcapitata ATHC TP9
## Mcapitata_ATHC_TP9_2862 Mcapitata_ATHC_TP9_2862 Mcapitata ATHC TP9
## Mcapitata_ATHC_TP9_2995 Mcapitata_ATHC_TP9_2995 Mcapitata ATHC TP9
## Mcapitata_ATHC_TP10_1204 Mcapitata_ATHC_TP10_1204 Mcapitata ATHC TP10
## Mcapitata_ATHC_TP10_2554 Mcapitata_ATHC_TP10_2554 Mcapitata ATHC TP10
## Mcapitata_ATHC_TP10_2737 Mcapitata_ATHC_TP10_2737 Mcapitata ATHC TP10
## Mcapitata_ATHC_TP11_1237 Mcapitata_ATHC_TP11_1237 Mcapitata ATHC TP11
## Mcapitata_ATHC_TP11_2188 Mcapitata_ATHC_TP11_2188 Mcapitata ATHC TP11
## Mcapitata_ATHC_TP11_2756 Mcapitata_ATHC_TP11_2756 Mcapitata ATHC TP11
## Mcapitata_ATHC_TP12_1154 Mcapitata_ATHC_TP12_1154 Mcapitata ATHC TP12
## Mcapitata_ATHC_TP12_2736 Mcapitata_ATHC_TP12_2736 Mcapitata ATHC TP12
## Mcapitata_ATHC_TP12_2990 Mcapitata_ATHC_TP12_2990 Mcapitata ATHC TP12
## Mcapitata_HTAC_TP1_1579 Mcapitata_HTAC_TP1_1579 Mcapitata HTAC TP1
## Mcapitata_HTAC_TP1_2153 Mcapitata_HTAC_TP1_2153 Mcapitata HTAC TP1
## Mcapitata_HTAC_TP1_2183 Mcapitata_HTAC_TP1_2183 Mcapitata HTAC TP1
## Mcapitata_HTAC_TP3_1289 Mcapitata_HTAC_TP3_1289 Mcapitata HTAC TP3
## Mcapitata_HTAC_TP3_1751 Mcapitata_HTAC_TP3_1751 Mcapitata HTAC TP3
## Mcapitata_HTAC_TP3_2021 Mcapitata_HTAC_TP3_2021 Mcapitata HTAC TP3
## Mcapitata_HTAC_TP4_1269 Mcapitata_HTAC_TP4_1269 Mcapitata HTAC TP4
## Mcapitata_HTAC_TP4_1481 Mcapitata_HTAC_TP4_1481 Mcapitata HTAC TP4
## Mcapitata_HTAC_TP4_2000 Mcapitata_HTAC_TP4_2000 Mcapitata HTAC TP4
## Mcapitata_HTAC_TP5_1321 Mcapitata_HTAC_TP5_1321 Mcapitata HTAC TP5
## Mcapitata_HTAC_TP5_1583 Mcapitata_HTAC_TP5_1583 Mcapitata HTAC TP5
## Mcapitata_HTAC_TP5_1997 Mcapitata_HTAC_TP5_1997 Mcapitata HTAC TP5
## Mcapitata_HTAC_TP6_1496 Mcapitata_HTAC_TP6_1496 Mcapitata HTAC TP6
## Mcapitata_HTAC_TP6_1588 Mcapitata_HTAC_TP6_1588 Mcapitata HTAC TP6
## Mcapitata_HTAC_TP6_1705 Mcapitata_HTAC_TP6_1705 Mcapitata HTAC TP6
## Mcapitata_HTAC_TP7_1278 Mcapitata_HTAC_TP7_1278 Mcapitata HTAC TP7
## Mcapitata_HTAC_TP7_1645 Mcapitata_HTAC_TP7_1645 Mcapitata HTAC TP7
## Mcapitata_HTAC_TP7_1722 Mcapitata_HTAC_TP7_1722 Mcapitata HTAC TP7
## Mcapitata_HTAC_TP8_1235 Mcapitata_HTAC_TP8_1235 Mcapitata HTAC TP8
## Mcapitata_HTAC_TP8_2386 Mcapitata_HTAC_TP8_2386 Mcapitata HTAC TP8
## Mcapitata_HTAC_TP8_2410 Mcapitata_HTAC_TP8_2410 Mcapitata HTAC TP8
## Mcapitata_HTAC_TP9_1306 Mcapitata_HTAC_TP9_1306 Mcapitata HTAC TP9
## Mcapitata_HTAC_TP9_1467 Mcapitata_HTAC_TP9_1467 Mcapitata HTAC TP9
## Mcapitata_HTAC_TP9_2412 Mcapitata_HTAC_TP9_2412 Mcapitata HTAC TP9
## Mcapitata_HTAC_TP10_1315 Mcapitata_HTAC_TP10_1315 Mcapitata HTAC TP10
## Mcapitata_HTAC_TP10_1478 Mcapitata_HTAC_TP10_1478 Mcapitata HTAC TP10
## Mcapitata_HTAC_TP10_1754 Mcapitata_HTAC_TP10_1754 Mcapitata HTAC TP10
## Mcapitata_HTAC_TP11_1248 Mcapitata_HTAC_TP11_1248 Mcapitata HTAC TP11
## Mcapitata_HTAC_TP11_1562 Mcapitata_HTAC_TP11_1562 Mcapitata HTAC TP11
## Mcapitata_HTAC_TP12_1632 Mcapitata_HTAC_TP12_1632 Mcapitata HTAC TP12
## Mcapitata_HTAC_TP12_1729 Mcapitata_HTAC_TP12_1729 Mcapitata HTAC TP12
## Mcapitata_HTAC_TP12_2007 Mcapitata_HTAC_TP12_2007 Mcapitata HTAC TP12
## Mcapitata_HTHC_TP1_1145 Mcapitata_HTHC_TP1_1145 Mcapitata HTHC TP1
## Mcapitata_HTHC_TP1_1323 Mcapitata_HTHC_TP1_1323 Mcapitata HTHC TP1
## Mcapitata_HTHC_TP1_2081 Mcapitata_HTHC_TP1_2081 Mcapitata HTHC TP1
## Mcapitata_HTHC_TP3_1128 Mcapitata_HTHC_TP3_1128 Mcapitata HTHC TP3
## Mcapitata_HTHC_TP3_1277 Mcapitata_HTHC_TP3_1277 Mcapitata HTHC TP3
## Mcapitata_HTHC_TP3_2518 Mcapitata_HTHC_TP3_2518 Mcapitata HTHC TP3
## Mcapitata_HTHC_TP4_1124 Mcapitata_HTHC_TP4_1124 Mcapitata HTHC TP4
## Mcapitata_HTHC_TP4_1328 Mcapitata_HTHC_TP4_1328 Mcapitata HTHC TP4
## Mcapitata_HTHC_TP4_2204 Mcapitata_HTHC_TP4_2204 Mcapitata HTHC TP4
## Mcapitata_HTHC_TP5_1345 Mcapitata_HTHC_TP5_1345 Mcapitata HTHC TP5
## Mcapitata_HTHC_TP5_1449 Mcapitata_HTHC_TP5_1449 Mcapitata HTHC TP5
## Mcapitata_HTHC_TP5_1694 Mcapitata_HTHC_TP5_1694 Mcapitata HTHC TP5
## Mcapitata_HTHC_TP6_1164 Mcapitata_HTHC_TP6_1164 Mcapitata HTHC TP6
## Mcapitata_HTHC_TP6_1317 Mcapitata_HTHC_TP6_1317 Mcapitata HTHC TP6
## Mcapitata_HTHC_TP6_1604 Mcapitata_HTHC_TP6_1604 Mcapitata HTHC TP6
## Mcapitata_HTHC_TP7_1126 Mcapitata_HTHC_TP7_1126 Mcapitata HTHC TP7
## Mcapitata_HTHC_TP7_1250 Mcapitata_HTHC_TP7_1250 Mcapitata HTHC TP7
## Mcapitata_HTHC_TP7_2419 Mcapitata_HTHC_TP7_2419 Mcapitata HTHC TP7
## Mcapitata_HTHC_TP8_1082 Mcapitata_HTHC_TP8_1082 Mcapitata HTHC TP8
## Mcapitata_HTHC_TP8_1246 Mcapitata_HTHC_TP8_1246 Mcapitata HTHC TP8
## Mcapitata_HTHC_TP8_2067 Mcapitata_HTHC_TP8_2067 Mcapitata HTHC TP8
## Mcapitata_HTHC_TP9_1078 Mcapitata_HTHC_TP9_1078 Mcapitata HTHC TP9
## Mcapitata_HTHC_TP9_1331 Mcapitata_HTHC_TP9_1331 Mcapitata HTHC TP9
## Mcapitata_HTHC_TP9_2009 Mcapitata_HTHC_TP9_2009 Mcapitata HTHC TP9
## Mcapitata_HTHC_TP10_1074 Mcapitata_HTHC_TP10_1074 Mcapitata HTHC TP10
## Mcapitata_HTHC_TP10_1332 Mcapitata_HTHC_TP10_1332 Mcapitata HTHC TP10
## Mcapitata_HTHC_TP10_1689 Mcapitata_HTHC_TP10_1689 Mcapitata HTHC TP10
## Mcapitata_HTHC_TP11_1178 Mcapitata_HTHC_TP11_1178 Mcapitata HTHC TP11
## Mcapitata_HTHC_TP11_1270 Mcapitata_HTHC_TP11_1270 Mcapitata HTHC TP11
## Mcapitata_HTHC_TP11_2511 Mcapitata_HTHC_TP11_2511 Mcapitata HTHC TP11
## Mcapitata_HTHC_TP12_1140 Mcapitata_HTHC_TP12_1140 Mcapitata HTHC TP12
## Mcapitata_HTHC_TP12_1274 Mcapitata_HTHC_TP12_1274 Mcapitata HTHC TP12
## Mcapitata_HTHC_TP12_2190 Mcapitata_HTHC_TP12_2190 Mcapitata HTHC TP12
## plugid reef reef_color ploidy ploidy_color
## Mcapitata_ATAC_TP11_2302 2302 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP11_2380 2380 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATAC_TP6_2402 2402 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATAC_TP12_2403 2403 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATAC_TP1_1037 1037 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP1_1600 1600 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP1_1652 1652 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP3_1101 1101 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP3_1548 1548 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATAC_TP3_1628 1628 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP4_1108 1108 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP4_1609 1609 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP4_1651 1651 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP5_1196 1196 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATAC_TP5_1610 1610 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP5_1776 1776 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP6_1114 1114 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP6_1611 1611 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP7_1058 1058 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_ATAC_TP7_1455 1455 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP7_1499 1499 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP8_1083 1083 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP8_1436 1436 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP8_1779 1779 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP9_1121 1121 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP9_1420 1420 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP9_1580 1580 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP10_1095 1095 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP10_1561 1561 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATAC_TP10_1631 1631 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP11_1076 1076 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATAC_TP11_1644 1644 HIMB #b35806 2 #01665e
## Mcapitata_ATAC_TP12_1120 1120 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATAC_TP12_1452 1452 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP1_1218 1218 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATHC_TP1_1826 1826 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATHC_TP1_2068 2068 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP3_1544 1544 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATHC_TP3_2731 2731 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP3_2866 2866 HIMB #b35806 2 #01665e
## Mcapitata_ATHC_TP4_1221 1221 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP4_2561 2561 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATHC_TP4_2734 2734 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP5_1229 1229 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP5_1706 1706 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATHC_TP5_2986 2986 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP6_1212 1212 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATHC_TP6_2016 2016 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP6_2555 2555 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATHC_TP7_1223 1223 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP7_2860 2860 HIMB #b35806 2 #01665e
## Mcapitata_ATHC_TP7_2875 2875 HIMB #b35806 2 #01665e
## Mcapitata_ATHC_TP8_1260 1260 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP8_2735 2735 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP8_2753 2753 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP9_1148 1148 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP9_2862 2862 HIMB #b35806 2 #01665e
## Mcapitata_ATHC_TP9_2995 2995 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATHC_TP10_1204 1204 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_ATHC_TP10_2554 2554 Reef.18 #d8daeb 2 #01665e
## Mcapitata_ATHC_TP10_2737 2737 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP11_1237 1237 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP11_2188 2188 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_ATHC_TP11_2756 2756 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP12_1154 1154 HIMB #b35806 2 #01665e
## Mcapitata_ATHC_TP12_2736 2736 Reef.42.43 #542788 2 #01665e
## Mcapitata_ATHC_TP12_2990 2990 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP1_1579 1579 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTAC_TP1_2153 2153 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP1_2183 2183 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTAC_TP3_1289 1289 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTAC_TP3_1751 1751 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTAC_TP3_2021 2021 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTAC_TP4_1269 1269 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTAC_TP4_1481 1481 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTAC_TP4_2000 2000 HIMB #b35806 2 #01665e
## Mcapitata_HTAC_TP5_1321 1321 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTAC_TP5_1583 1583 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTAC_TP5_1997 1997 HIMB #b35806 2 #01665e
## Mcapitata_HTAC_TP6_1496 1496 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTAC_TP6_1588 1588 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP6_1705 1705 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTAC_TP7_1278 1278 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTAC_TP7_1645 1645 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTAC_TP7_1722 1722 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTAC_TP8_1235 1235 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTAC_TP8_2386 2386 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP8_2410 2410 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP9_1306 1306 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTAC_TP9_1467 1467 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTAC_TP9_2412 2412 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP10_1315 1315 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTAC_TP10_1478 1478 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTAC_TP10_1754 1754 HIMB #b35806 2 #01665e
## Mcapitata_HTAC_TP11_1248 1248 HIMB #b35806 2 #01665e
## Mcapitata_HTAC_TP11_1562 1562 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTAC_TP12_1632 1632 HIMB #b35806 4 #7570b3
## Mcapitata_HTAC_TP12_1729 1729 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTAC_TP12_2007 2007 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTHC_TP1_1145 1145 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP1_1323 1323 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTHC_TP1_2081 2081 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP3_1128 1128 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP3_1277 1277 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP3_2518 2518 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTHC_TP4_1124 1124 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTHC_TP4_1328 1328 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP4_2204 2204 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTHC_TP5_1345 1345 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTHC_TP5_1449 1449 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTHC_TP5_1694 1694 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP6_1164 1164 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTHC_TP6_1317 1317 Reef.35.36 #998ec3 2 #01665e
## Mcapitata_HTHC_TP6_1604 1604 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP7_1126 1126 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTHC_TP7_1250 1250 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTHC_TP7_2419 2419 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTHC_TP8_1082 1082 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP8_1246 1246 Reef.42.43 #542788 2 #01665e
## Mcapitata_HTHC_TP8_2067 2067 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP9_1078 1078 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP9_1331 1331 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP9_2009 2009 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTHC_TP10_1074 1074 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP10_1332 1332 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP10_1689 1689 Reef.11.13 #fee0b6 2 #01665e
## Mcapitata_HTHC_TP11_1178 1178 Lilipuna.Fringe #f1a340 2 #01665e
## Mcapitata_HTHC_TP11_1270 1270 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP11_2511 2511 Reef.18 #d8daeb 2 #01665e
## Mcapitata_HTHC_TP12_1140 1140 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP12_1274 1274 HIMB #b35806 2 #01665e
## Mcapitata_HTHC_TP12_2190 2190 Reef.42.43 #542788 2 #01665e
## group group_color
## Mcapitata_ATAC_TP11_2302 Group1 #1f78b4
## Mcapitata_HTAC_TP11_2380 Group1 #1f78b4
## Mcapitata_ATAC_TP6_2402 Group2 #33a02c
## Mcapitata_ATAC_TP12_2403 Group2 #33a02c
## Mcapitata_ATAC_TP1_1037 Ungrouped #808080
## Mcapitata_ATAC_TP1_1600 Ungrouped #808080
## Mcapitata_ATAC_TP1_1652 Ungrouped #808080
## Mcapitata_ATAC_TP3_1101 Ungrouped #808080
## Mcapitata_ATAC_TP3_1548 Ungrouped #808080
## Mcapitata_ATAC_TP3_1628 Ungrouped #808080
## Mcapitata_ATAC_TP4_1108 Ungrouped #808080
## Mcapitata_ATAC_TP4_1609 Ungrouped #808080
## Mcapitata_ATAC_TP4_1651 Ungrouped #808080
## Mcapitata_ATAC_TP5_1196 Ungrouped #808080
## Mcapitata_ATAC_TP5_1610 Ungrouped #808080
## Mcapitata_ATAC_TP5_1776 Ungrouped #808080
## Mcapitata_ATAC_TP6_1114 Ungrouped #808080
## Mcapitata_ATAC_TP6_1611 Ungrouped #808080
## Mcapitata_ATAC_TP7_1058 Ungrouped #808080
## Mcapitata_ATAC_TP7_1455 Ungrouped #808080
## Mcapitata_ATAC_TP7_1499 Ungrouped #808080
## Mcapitata_ATAC_TP8_1083 Ungrouped #808080
## Mcapitata_ATAC_TP8_1436 Ungrouped #808080
## Mcapitata_ATAC_TP8_1779 Ungrouped #808080
## Mcapitata_ATAC_TP9_1121 Ungrouped #808080
## Mcapitata_ATAC_TP9_1420 Ungrouped #808080
## Mcapitata_ATAC_TP9_1580 Ungrouped #808080
## Mcapitata_ATAC_TP10_1095 Ungrouped #808080
## Mcapitata_ATAC_TP10_1561 Ungrouped #808080
## Mcapitata_ATAC_TP10_1631 Ungrouped #808080
## Mcapitata_ATAC_TP11_1076 Ungrouped #808080
## Mcapitata_ATAC_TP11_1644 Ungrouped #808080
## Mcapitata_ATAC_TP12_1120 Ungrouped #808080
## Mcapitata_ATAC_TP12_1452 Ungrouped #808080
## Mcapitata_ATHC_TP1_1218 Ungrouped #808080
## Mcapitata_ATHC_TP1_1826 Ungrouped #808080
## Mcapitata_ATHC_TP1_2068 Ungrouped #808080
## Mcapitata_ATHC_TP3_1544 Ungrouped #808080
## Mcapitata_ATHC_TP3_2731 Ungrouped #808080
## Mcapitata_ATHC_TP3_2866 Ungrouped #808080
## Mcapitata_ATHC_TP4_1221 Ungrouped #808080
## Mcapitata_ATHC_TP4_2561 Ungrouped #808080
## Mcapitata_ATHC_TP4_2734 Ungrouped #808080
## Mcapitata_ATHC_TP5_1229 Ungrouped #808080
## Mcapitata_ATHC_TP5_1706 Ungrouped #808080
## Mcapitata_ATHC_TP5_2986 Ungrouped #808080
## Mcapitata_ATHC_TP6_1212 Ungrouped #808080
## Mcapitata_ATHC_TP6_2016 Ungrouped #808080
## Mcapitata_ATHC_TP6_2555 Ungrouped #808080
## Mcapitata_ATHC_TP7_1223 Ungrouped #808080
## Mcapitata_ATHC_TP7_2860 Ungrouped #808080
## Mcapitata_ATHC_TP7_2875 Ungrouped #808080
## Mcapitata_ATHC_TP8_1260 Ungrouped #808080
## Mcapitata_ATHC_TP8_2735 Ungrouped #808080
## Mcapitata_ATHC_TP8_2753 Ungrouped #808080
## Mcapitata_ATHC_TP9_1148 Ungrouped #808080
## Mcapitata_ATHC_TP9_2862 Ungrouped #808080
## Mcapitata_ATHC_TP9_2995 Ungrouped #808080
## Mcapitata_ATHC_TP10_1204 Ungrouped #808080
## Mcapitata_ATHC_TP10_2554 Ungrouped #808080
## Mcapitata_ATHC_TP10_2737 Ungrouped #808080
## Mcapitata_ATHC_TP11_1237 Ungrouped #808080
## Mcapitata_ATHC_TP11_2188 Ungrouped #808080
## Mcapitata_ATHC_TP11_2756 Ungrouped #808080
## Mcapitata_ATHC_TP12_1154 Ungrouped #808080
## Mcapitata_ATHC_TP12_2736 Ungrouped #808080
## Mcapitata_ATHC_TP12_2990 Ungrouped #808080
## Mcapitata_HTAC_TP1_1579 Ungrouped #808080
## Mcapitata_HTAC_TP1_2153 Ungrouped #808080
## Mcapitata_HTAC_TP1_2183 Ungrouped #808080
## Mcapitata_HTAC_TP3_1289 Ungrouped #808080
## Mcapitata_HTAC_TP3_1751 Ungrouped #808080
## Mcapitata_HTAC_TP3_2021 Ungrouped #808080
## Mcapitata_HTAC_TP4_1269 Ungrouped #808080
## Mcapitata_HTAC_TP4_1481 Ungrouped #808080
## Mcapitata_HTAC_TP4_2000 Ungrouped #808080
## Mcapitata_HTAC_TP5_1321 Ungrouped #808080
## Mcapitata_HTAC_TP5_1583 Ungrouped #808080
## Mcapitata_HTAC_TP5_1997 Ungrouped #808080
## Mcapitata_HTAC_TP6_1496 Ungrouped #808080
## Mcapitata_HTAC_TP6_1588 Ungrouped #808080
## Mcapitata_HTAC_TP6_1705 Ungrouped #808080
## Mcapitata_HTAC_TP7_1278 Ungrouped #808080
## Mcapitata_HTAC_TP7_1645 Ungrouped #808080
## Mcapitata_HTAC_TP7_1722 Ungrouped #808080
## Mcapitata_HTAC_TP8_1235 Ungrouped #808080
## Mcapitata_HTAC_TP8_2386 Ungrouped #808080
## Mcapitata_HTAC_TP8_2410 Ungrouped #808080
## Mcapitata_HTAC_TP9_1306 Ungrouped #808080
## Mcapitata_HTAC_TP9_1467 Ungrouped #808080
## Mcapitata_HTAC_TP9_2412 Ungrouped #808080
## Mcapitata_HTAC_TP10_1315 Ungrouped #808080
## Mcapitata_HTAC_TP10_1478 Ungrouped #808080
## Mcapitata_HTAC_TP10_1754 Ungrouped #808080
## Mcapitata_HTAC_TP11_1248 Ungrouped #808080
## Mcapitata_HTAC_TP11_1562 Ungrouped #808080
## Mcapitata_HTAC_TP12_1632 Ungrouped #808080
## Mcapitata_HTAC_TP12_1729 Ungrouped #808080
## Mcapitata_HTAC_TP12_2007 Ungrouped #808080
## Mcapitata_HTHC_TP1_1145 Ungrouped #808080
## Mcapitata_HTHC_TP1_1323 Ungrouped #808080
## Mcapitata_HTHC_TP1_2081 Ungrouped #808080
## Mcapitata_HTHC_TP3_1128 Ungrouped #808080
## Mcapitata_HTHC_TP3_1277 Ungrouped #808080
## Mcapitata_HTHC_TP3_2518 Ungrouped #808080
## Mcapitata_HTHC_TP4_1124 Ungrouped #808080
## Mcapitata_HTHC_TP4_1328 Ungrouped #808080
## Mcapitata_HTHC_TP4_2204 Ungrouped #808080
## Mcapitata_HTHC_TP5_1345 Ungrouped #808080
## Mcapitata_HTHC_TP5_1449 Ungrouped #808080
## Mcapitata_HTHC_TP5_1694 Ungrouped #808080
## Mcapitata_HTHC_TP6_1164 Ungrouped #808080
## Mcapitata_HTHC_TP6_1317 Ungrouped #808080
## Mcapitata_HTHC_TP6_1604 Ungrouped #808080
## Mcapitata_HTHC_TP7_1126 Ungrouped #808080
## Mcapitata_HTHC_TP7_1250 Ungrouped #808080
## Mcapitata_HTHC_TP7_2419 Ungrouped #808080
## Mcapitata_HTHC_TP8_1082 Ungrouped #808080
## Mcapitata_HTHC_TP8_1246 Ungrouped #808080
## Mcapitata_HTHC_TP8_2067 Ungrouped #808080
## Mcapitata_HTHC_TP9_1078 Ungrouped #808080
## Mcapitata_HTHC_TP9_1331 Ungrouped #808080
## Mcapitata_HTHC_TP9_2009 Ungrouped #808080
## Mcapitata_HTHC_TP10_1074 Ungrouped #808080
## Mcapitata_HTHC_TP10_1332 Ungrouped #808080
## Mcapitata_HTHC_TP10_1689 Ungrouped #808080
## Mcapitata_HTHC_TP11_1178 Ungrouped #808080
## Mcapitata_HTHC_TP11_1270 Ungrouped #808080
## Mcapitata_HTHC_TP11_2511 Ungrouped #808080
## Mcapitata_HTHC_TP12_1140 Ungrouped #808080
## Mcapitata_HTHC_TP12_1274 Ungrouped #808080
## Mcapitata_HTHC_TP12_2190 Ungrouped #808080
Load pairwise percent shared SNP results and convert if from one line per pair format into a symetric matrix uisng the xtabs function.
pairwise_percent_shared <- read.table("GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.tsv", sep='\t', header=T)
pairwise_percent_shared.matrix <- xtabs(match_perc ~ ind1 + ind2, data=pairwise_percent_shared)
Process the simScore data ready for plotting (i.e., cluster samples based on computed distance and construct a dendrogram of the relationship).
# Make a copy of input matrix
tmp.mat <- pairwise_percent_shared.matrix
# Generate clusters from the allelic similarity scores matrix
tmp.mat.dist <- dist(tmp.mat, method="euclidean")
tmp.mat.hclust <- hclust(tmp.mat.dist, method="complete")
# Get sample colors for sidebar in the same order as the matrix
Rcols <- samples.info[rownames(tmp.mat),]$group_color
Ccols <- samples.info[colnames(tmp.mat),]$group_color
# Get min and max values of matrix
tmp.mat.min <- min(tmp.mat); tmp.mat.min
## [1] 79.16
tmp.mat.max <- max(tmp.mat); tmp.mat.max
## [1] 100
Plot clustering results and write dendrogram to file.
simScore.dendro <- as.dendrogram(tmp.mat.hclust)
write.dendrogram(simScore.dendro, "cluster_dendrogram.tre", edges=TRUE)
plot(tmp.mat.hclust)
Write ordered matrix to file incase we want it later.
tmp.mat.order <- dendro_data(simScore.dendro, type="rectangle")[["labels"]][["label"]]
tmp.mat.ordered <- tmp.mat[
order(match(rownames(tmp.mat), rev(tmp.mat.order))),
order(match(colnames(tmp.mat), tmp.mat.order))
]
write.table(as.matrix(tmp.mat.ordered),
"GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.matrix.tsv",
sep='\t', quote=FALSE,
row.names=TRUE, col.names=TRUE)
Plot simScores heatmap.
par(cex.main=0.7, cex.lab=0.9, cex.axis=0.9) # Change the font size of the legend title, labels and axis
heatmap.2(x=tmp.mat,
Rowv = simScore.dendro,
Colv = simScore.dendro,
col=cividis(length(seq(75, 100, 0.1))-1),
breaks=seq(75, 100, 0.1),
trace="none", # Dont draw "trace" line
key=TRUE, # Show color-key
margins=c(8,8), # Numeric vector of length 2 containing the margins for column and row names, respectively.
ColSideColors=Ccols,
RowSideColors=Rcols,
offsetRow=0,
offsetCol=0,
cexRow=cexSize, # Positive numbers, used as cex.axis in for the row or column axis labeling.
cexCol=cexSize,
cellnote=formatC(tmp.mat, big.mark=","),
notecex=0.1,
)